This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Software tools for sequence alignments and structure homology modeling must evolve with the large volume of new data being produced by the various genome projects and technologies such as DNA microarrays. Many of the commonly used bioinformatics programs have yet to take advantage of the technological advances made in areas such as Python, Java, and web-based interfaces. We have designed and implemented programs to take advantage of these new technologies to enable the informaticist/scientist to have a more user-friendly and efficient working environment. Our software tools help automate the data processing pipeline for sequence data and the facile management of results. We are designing Perl and Python applications for molecular biologists interested in structure studies in order to make the wealth of available UNIX sequence analysis and homology modeling tools as easy to use as browsing the Web. Further, we intend to develop automated analysis tools for many of the more routine data analysis tasks. The Resource for Biocomputing, Visualization, and Informatics (RBVI) offers a unique context for this interdisciplinary work, and though our collaborations with molecular biologists and other scientists the tools we develop are having an important impact on the broader scientific community.